We have purified specific DNA methylating enzymes from a variety of Haemophilus species capable of methylating eukaryotic DNA at specific cytosine containing locii in cell-free reactions. Additionally, we have partly characterized the enzymatic assay as to its reaction kinetics and substrates: S-adenosylmethionine (S-AM) and a variety of DNAs both prokaryotic, viral and eukaryotic species. The methylated DNA products of the cell-free reaction are essentially completely protected from the corresponding restriction-endonuclease catalyzed cleavaged and become useful probes as to the effects of site specific DNA modification vis-a-vis the efficacy of the modified DNA to perform a genetic function at a cellular level. Towards this end we have shown that certain specific locii of recombinant DNA vectors containing eukaryotic retroviral sequences are sensitive to specific methylase modifications. Specifically, certain methylated modification reduces the efficiency of cellular neoplastic transformation normally catalyzed by the retroviral sequences. Using a variety of methylated recombinant DNA constructs, we have been able to determine that hypermethylated retroviral DNA is less effective at promoting neoplastic cellular changes in vitro than its hypomethylated counterpart.